Projects

A unique 75-million-yr-old window into the ecology of Cretaceous forests during the rise of flowering plants
UCB team: Dori Contreras (now with the Perot Museum of Nature and Science, TX), Jaemin Lee & Cindy Looy
Collaborators: Gary Upchurch (Texas State U); Elizabeth Wheeler (North Carolina State U); Emilio Estrada-Ruiz (Instituto Politécnico Nacional, Mexico); James Doyle (UC Davis) & Selena Smith (U of Michigan)
Undergraduate student researchers: Grant Nguyen, Kelly Morgan, Reine Ngnonsse & Sam Bi
Sponsored by the National Science Foundation
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Jaemin and Dori digitizing and morphotyping approximately one gazillion Jose Creek fossil specimens in the bowels of the UCMP.
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Sample platter of some of the many leaf fossils in the Jose Creek flora, including palm and fern fronds, foliated conifer shoots and dicot and monocot angiosperm leaves.
Tropical forests are important hotspots of biodiversity, harboring unparalleled numbers of plant and animal species. The high diversity of modern tropical forests is due to the dominance of flowering plants, which first appeared ~140 million years ago (mya) during the age of dinosaurs. Flowering plants rapidly diversified and spread around the globe during the remainder of the Cretaceous (140-66 mya), and evolved a variety of life forms that added to the ecological complexity of forests.

This project investigates a crucial interval of the vegetational transition, ~75 million years ago. The late Cretaceous (100.5-66 million years ago) was a critical transition in Earth history, and the dawn of modern forests as we know them, yet the timing and sequence of many key events remains unanswered. We use extensive paleontological field studies, fossil collections, and new quantitative techniques to generate comprehensive reconstructions of this late Campanian forest from fossilized leaves, wood, and reproductive materials (including seeds, fruits, cones, and flowers). The fossil flora is from the Jose Creek Member of the McRae Formation in south-central New Mexico, which was located >200 km inland of the Western Interior Seaway — an inland sea that covered large parts of central North America. These plant assemblages provide an unprecedented opportunity because — unlike most similarly-aged fossil floras — they are from interior, rather than coastal or swampy environments, and represent tropical, rather than cooler climatic conditions. The plant remains are encased in a layer of volcanic ash. As the ash fell, it 'collected' and entombed plant bits from the top of the canopy down to the understory, and as such sampled and preserved multiple plant organs in close association from throughout the vertically tiered forest structure. An outcrop of the fossiliferous ash deposit can be traced for 1.2 km through the New Mexican landscape and thus represents a linear transect through the former forest ecosystem — documenting the geographic patchiness of its structure at a sub-ecosystem scale. Reconstruction of the flora from leaf macrofossils has provided the first quantitative evidence that ecological dominance of flowering plants was established by the late Campanian in warmer climates, and that this flora is the most speciose single-deposit Cretaceous flora known to date. By using newly developed sampling and analytical techniques, these studies will generate high-resolution reconstructions of the diversity and ecological structure of the paleoforest. In addition, the project will provide important insights into forest evolution in tropical climates, the timing and patterns of ecological expansion of flowering plants, the habitats of dinosaurs and early mammals, and the history of vegetation for the Western-Interior of North America.
Currently, graduate student Jaemin Lee is working on the ecology of seeds and fruits, description of flowers and inflorescences/infructescences, and quantitative study of leaf herbivory by arthropods, with undergraduate research assistants Sam Bi and Kelly Morgan. The diaspore sizes (plant dispersal unit) show a significant departure from other Cretaceous floras in previous studies, suggesting that the flowering plants in this late Campanian flora had more diverse diaspore morphologies and associated dispersal strategies. The insect damage analysis will provide insight into plant-insect interactions during this crucial period of taxonomic turnover, and will clarify important aspects of the fossil forest ecosystem structure by adding herbivorous insects and pollinators into the picture. Moreover, some specialized leaf damage types (e.g., galls and mines) are taxonomically identifiable, and will thus provide indirect evidence of the abundance of some specific insect taxa — even in the absence of body fossils of those taxa.

Publications: Contreras DL, 2018. A workflow and protocol describing the field to digitization process for new project-based fossil leaf collections. Applications in Plant Sciences6(2): e1025. https://doi.org/10.1002/aps3.1025 
Testing UV-B radiation as a proposed driver behind the end-Permian biotic crisis
UCB team: Jeff Benca (now with the Burke Museum of Natural History and Culture, WA), Sunita Bohara, Cindy Looy & Ivo Duijnstee
Collaborators: Henrik Svensen & Sverre Planke (U of Oslo, Norway); Alexander Polozov (Russian Academy of Sciences); Barry Lomax & Matthew Kent (U of Nottingham, UK); Surangi Punyasena (U of Illinois, Champaign-Urbana)
Sponsored by the National Science Foundation
The ozone layer plays a vital role in intercepting harmful solar ultraviolet-B radiation (UV-B) from reaching Earth’s surface. However, its effectiveness in doing so has fluctuated in the past and little is known of the impacts of a thinning ozone layer on vegetation.

Anticipating potential consequences in the future depends on understanding time intervals with heightened UV stress in the past. The largest mass extinction in history at the end of the Permian Period (~252 million years ago) and associated biotic crises may have encompassed such time intervals. Plant fossil records from these crises show two odd features worldwide. Many pollen grains produced by vanishing woodland seed plants were malformed, and proliferating herbaceous plants (lycopsids) spread their spores frequently as unseparated clusters of four. Heightened UV exposure is hypothesized to have caused these abnormalities. Compounds produced by the largest volcanic province in history, the Siberian Traps, likely caused prolonged or frequent deterioration of the ozone shield. We are testing if high UV-B radiation levels could indeed explain the abnormalities and extinction patterns in plants observed during the end-Permian biotic crisis using growth chamber and germination experiments and compare these with end-Permian fossil pollen and spore assemblages from sediments within the Siberian Traps.

Publications:
Benca JP, Duijnstee IAP, CV Looy, 2018. UV-B-induced malformed pollen implicates ozone shield failure in Earth's largest mass extinction. Science Advances 4: e1700618 doi.org/10.1126/sciadv.1700618 (pdf file here)

Benca JP, Duijnstee IAP and Looy CV, 2022. Pollen malformations as indicators of past environmental stress: Comparing background variation with heightened UV-B exposure in modern conifers. Paleobiology. 34 pp. doi.org/10.1017/pab.2022.3
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Watch Jeff explain his UV-B experiments with miniature Pinus mugo pine trees. (video by Roxanne Makasdjian & Stephen McNally, © Berkeley News)
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Range of UV-B-induced malformations of pollen in Pinus mugo
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Developing ovuliferous cones (no UV-B and outdoor control) versus early stage termination of ovuliferous cone development under elevated UV-B levels
Using fossils to better understand periods of global warming in Earth's past
UCB team: Jenn Wagner & Cindy Looy
Collaborators: Lenny Kouwenberg (Utrecht, The Netherlands), Lauren Michel (Tennessee Tech) & Joe Milligan (Baylor University, TX)
Undergraduate student researchers: Riya Tandon plus former students Josie Christon, Isha Mahajan, Tanmayi Patharkar
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Light level during development of leaves has a marked effect on the shape and size of epidermal cells, as illustrated here in leaves of the American sycamore (Platanus occidentalis). The two image above show microscope photographs (at the same magnification) of cleared sycamore leaves, grown under different light conditions by Lenny Kouwenberg at the Field Museum in Chicago. Note how the cells of the low-light-grown leaf (bottom) are much larger with much wavier (undulated) cell walls than the high-light-grown leaf (top).
Plants are adapted to the physical conditions of the environments they live in, including temperature, precipitation, atmospheric CO2 concentrations, and light level. In cooler and drier habitats, leaves tend to be smaller with condensed venation and toothed margins. While under warmer and wetter conditions, leaves tend to be larger, have ‘drip tips’, and entire margins. Atmospheric CO2 concentration and light regulate leaf size, stomatal patterns, and cell shape in developing leaves. These characteristics are preserved in the plant fossil record—for instance in cuticles, the decay-resistant waxy layer that envelops leaves—and can be used to infer local conditions at the time the plants were alive. We use this kind of information to better understand Earth’s history, the evolution of ecosystems, and to help predict the effects of global warming.

To assess changes in plant community composition and distribution during periods of long term and rapid global warming we are studying global warming in the early Paleogene. During the early Paleogene, the Earth experienced a long-term global temperature increase (~58–52 million years ago) punctuated by multiple hyperthermal (extra hot) events. As the poles warm more than the tropics, the warming resulted in a reduction of the latitudinal temperature gradient in addition to a global increase in seasonality and drought. Changes in faunal and floral distribution and composition have been well-documented in the western part of North America and other regions during this time period. Several studies have supported the hypothesis that a widespread band of thermophilic plant communities existed and expanded into the mid latitudes, consistent with biota tracking climate change. However, it is not clear how well these floras are connected, and how exactly they responded during these rapid and long-term global warming events.

This project investigates the response of Eocene Gulf Coastal Plain (GCP) plant communities to these warming events using cuticular analysis, various leaf physiognomic traits (e.g., digital leaf physiognomy or DiLP, leaf mass per area, leaf margin analysis, leaf area analysis, and leaf area index), and systematic census collections of several fossil floras. In parallel, we study living plants—grown under various controlled conditions—to understand how plant physiognomy is affected by environmental change.

Jenn worked on cuticular analysis of oak and sycamore leaves to better understand the relationships among light level and various leaf morphological characteristics. In addition, Jenn is using Eocene leaf cuticle (located in the UCMP) collected from the Claiborne formation in Tennessee, while during recent field seasons, they have been revisiting and collecting floras from several well-preserved GCP floras from the Claiborne group in Tennessee and Kentucky. Besides taxonomy-based specimen collection, also systematic census collections will be made wherever possible to assess diversity and community composition.
Publication: Milligan JN, Flynn AG, Wagner JD, Kouwenberg LL, Barclay RS, Byars BW, Dunn RE, White JD, Zechmann B and Peppe DJ, 2021. Quantifying the effect of shade on cuticle morphology and carbon isotopes of sycamores: present and past. American journal of botany 108: 2435–2451. doi.org/10.1002/ajb2.1772
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Collecting exquisitely preserved leaf fossils from the Eocene (56–33.9 million years ago) in the Hickory Clay Mining Co quarry. Jenn and their research apprentice Josie were joined in the field by Dr. Lauren Michel and Britney McGuire from Tennessee Tech.
The foundation of terrestrial life: inferring a total-evidence timeline of vascular plant evolution
UCB team: Mike May, Dori Contreras (now Perot Museum of Nature and Science), Ben Muddiman, Cindy Looy & Carl Rothfels
Collaborators: Nathalie Nagalingum (Cal Academy of Sci), Michael Sundue (Pringle Herbarium, VT) & Ryan Thummel (Vancouver, BC)
Undergraduate student researcher: Lan Wei
Sponsored by the National Science Foundation
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A hypothetical total-evidence timeline of selected fossil and extant vascular plants, showing major lineages, possible relationships and divergence times. Outgroups comprise the three extant bryophyte lineages. Horizontal grey lines mark the 100-million-year intervals; dashed red lines mark the end-Cretaceous and end-Permian mass extinctions. Time period abbreviations follow standard IUGS names. Tree topology, fossil ages, and divergence times are synthesized from the literature, particularly Wikström et al. (2001), Taylor et al. (2009), and Rothfels et al. (2015b).
This project will determine when vascular plants evolved and how they are related. Vascular plants include lycopods, ferns and their allies, as well as conifers and flowering plants. They form the foundation of nearly all terrestrial ecosystems and our food supply, yet scientists disagree about when and how they evolved. Current methods for estimating evolutionary timelines for these species have led to conflicting answers, as they rely on the ability of researchers to assign extinct fossil species correctly to particular branch points in the tree of life. This assignment is challenging to do because extinct species may have morphology that can be interpreted differently. We will refine a new data analysis method to address this limitation and compare the DNA sequences of living vascular plants and incorporate morphological data from both living and extinct species to reconstruct their evolutionary relationships. 
Tuning the pollen and spore records of Permian Gondwana: deciphering the history of terrestrial ecosystem response during the late Paleozoic deglaciation
UCB team: Riley Hayes & Cindy Looy
Only once before today have icecaps and complex terrestrial ecosystems coexisted on Earth: the Late Paleozoic Ice Age (ca. 340-280 million years ago). While the ocean-covered north pole lacked land ice, one or multiple icecaps covered large parts of Gondwana, a southern-hemisphere landmass comprised of South America, Africa, Australia, Antarctica, and India. Plant fossils—especially pollen and spores—record plant migrations and changes in ecosystems worldwide following the gradual decline of the ice masses. Just as today, available evidence implicates CO2-forcing as the cause of this planetary-scale deglaciation.

Pollen and spore fossils from the Permian of Gondwana constitute the only high-resolution prior record of high-latitude plant communities during an icehouse-to-greenhouse transition. However, the difficulty of precisely correlating these fossil records to the international geologic time scale obscures the tempo of floral change during this interval. No quantitative model capable of detecting rapid vegetation fluctuations contemporaneous with the Gondwanan deglaciation presently exists.

We aim to develop tools suitable for the task: high-precision timescales of the Permian of Australia, derived from the rich record of fossil pollen and spores preserved in sedimentary basins across the continent. The timescale is derived via constrained optimization algorithms, implemented in the software CONOP9. These algorithms first draw upon pollen and spore records to assemble a scaled composite sequence of fossil first and last appearance datums. Next, high-precision zircon dates (U-Pb CA-TIMS) directly associated with those fossil records calibrate the timescales, yielding high-resolution records of vegetation change.

Preliminary work shows that the model uniquely illustrates trends in the diversity and biogeography of high-latitude vegetation during an unparalleled historical precedent to the ongoing human-induced icehouse-to-greenhouse transition.
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252-million-year-old pollen and spores from South Africa. Hot volcanic intrusions cause these microfossils to be poorly preserved, but fortunately they remain recognizable.
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Graphic representation of CONOP9's optimization process of known palynological records, as it iteratively works towards an optimal fossil-based timescale for palynomorphs in late Paleozoic Gondwana. Horizontal lines represent hypothetical temporal ranges of pollen and spore types, whereas yellow specks above denote zircon ages and stratigraphic constraints. The downward-trending, erratic white line depicts the progress of the search, with the green dots along it denoting the most optimal timescales discovered so far.
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Zircon crystals such as these tell us how old pollen-and-spore-yielding sediments are. After they are formed in volcanic magma chambers, the nuclear decay clock of incorporated radioactive elements in the crystals starts ticking. By measuring concentrations of decay products relative to the remaining unstable source material in very nifty and sophisticated ways, geochronologists can work out the absolute age of the crystal—thus providing a maximum age for the sediments they were found in (image courtesy of Sandra Kamo, University of Toronto).
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A biogeographic network of Gondwanan floras during the Guadalupian epoch of the Permian (~273-259 million years ago), based on a preliminary CONOP9 timescale. Colors represent plant assemblages characterizing distinct floral provinces across Gondwana. In the near future we will reconstruct how these floral provinces moved poleward and to how their composition changed.
The Phillips Coal Ball Collection treasure trove: Reconstructing wildfire from a lost, hyperoxic world, preserved in the most detailed plant fossil collection ever
UCB team (lead institution): Ben Muddiman, Cindy Looy & Ivo Duijnstee
Collaborators: Scott Elrick & John Nelson (Illinois State Geological Survey), Bill DiMichele (National Museum of Natural History), Mike Donovan (Field Museum), Surangi Punyasena, Scott Lakeram & Max Christie (University of Illinois Urbana-Champaign)
Former undergraduate student researchers: Henry Thomas & Sydney Booth
Sponsored by a Chemical Society of America PRF Grant
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From left to right: (1) The late Tom L. Phillips, students and colleagues on a coal ball collection expedition in an open coal mine in Southern Illinois, 1968 (photo courtesy Dr. Hermann Pfefferkorn). (2) Five decades later, Tom Phillips and his former student Bill DiMichele—staring into a so-called discussion microscope to compare notes on the anatomically preserved plant tissues, embedded in a coal ball acetate peel. (3) Enumerating plant taxa, organs and tissues square cm by square cm (more than a mind-boggling 800,000 cm2 have thus been assessed by Phillips, his students and collaborators).
The Carboniferous (359-299 million years ago) is an exceptionally interesting period in Earth’s history. Geographically, ecologically, atmospherically, and climatically, the world was unlike anything we see today. What are now Europe and America were one landmass—Euramerica, in the equatorial region of the supercontinent Pangea, which contained all 7 current continents. Unlike today, Euramerica was largely a flat craton, a landscape with little topography. In the later parts of the Carboniferous, the craton was periodically dominated by widespread peat swamps. These swamps were often dominated by tall (>100 ft) spore-bearing lycopod trees, making for an alien looking, Dr. Seuss-like landscape.

Interestingly, the Carboniferous was also a period of cyclic, recurring episodes of climate change—quite similar to the glacial-interglacial alternations that our planet has experienced in the last few millions of years. In the Euramerican tropics this Late Paleozoic Ice Age resulted in an everwet climate during the glacial period and  a seasonally dry climate during the interglacials. These glacial-interglacial cycles occurred over 30 times, making this a great period to study the impacts of climate change on ecosystems.

Paleofire
From an atmospheric perspective, oxygen levels were likely significantly higher than the Present Atmospheric Level of ~21%. This so-called hyperoxic atmosphere would have impacted the physiology of plants and animals (possibly contributing to the enormous size of some insects). We think that it also changed the prevalence of fire—the hyperoxia likely led to increased fire frequency and intensity. Experimental work shows that ignition probability, fire spread rate, and burn duration all increase with rising oxygen levels. How these changes in the physics of fire were manifested in the peat swamp ecosystems of the Late Carboniferous is largely still a mystery.

Reconstructing the behavior and impact of fires on these ancient landscapes is no easy task. The biggest single treasure trove of exquisitely preserved plant fossils ever collected on our planet—the Tom Phillips Coal Ball Collection and database (for more on this, look here and here)—contains detailed information on not only the abundance of fossilized charcoal—our best evidence of paleofire—through space and time, but also information on which plant groups and which organs (leaves, roots, reproductive parts, etc.) burned. These data will allow us to link our understanding of the physical changes in fire under hyperoxic conditions with the ecosystem impacts that these fires had. Because this dataset covers millions of years of fossil material, we can also relate changes in fire frequency, behavior, and impact to the dramatic climatic shifts that happened repeatedly in the Carboniferous.

Why should you care?
Understanding the impacts of climate change on plant communities and on fire frequency, distribution, intensity, etc. is an important undertaking given current projections for Earth’s future climate. Especially now the west coast of North America seems to have entered a new era of annual megafires, this is of course of great interest.
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Detail from a reconstruction of a Pennsylvanian peat swamp landscape by Alice Prickett; commissioned by Tom Phillips for a publication on “Paleobotany and paleoecology of coal” (Phillips & Cross, 1991).
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Ready to peel: >300-million-yr-old coal balls (carbonate nodules encasing peat material) in the Phillips Lab the University of Illinois Urbana-Champaign (UIUC). The coal balls were cut in half, and adhering to the polished and etched surfaces are the shiny, transparent acetate sheets that have embedded the cell walls of fossil plant tissues that were standing just proud of the etched carbonate surface.
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In the Phillips coal ball warehouse on the UIUC campus, Ben Muddiman shows a coal ball peal on a standardized cm x cm grid that was used to enumerate plant taxa, organs and tissues preserved in the coal balls.
The Pteridological Collections Consortium: an integrative approach to pteridophyte diversity over the last 420 million years
UCB team (lead institution): Diane Erwin, Amy Kasameyer, Joyce Gross, Cindy Looy & Carl Rothfels
Collaborators: many PIs from 35 herbaria and museums in the USA
Sponsored by a National Science Foundation ADBC Grant
Pteridophytes (ferns, lycophytes, and their extinct free-sporing relatives) are a diverse group of plants that today comprises approximately 12,000 species and plays a major role in terrestrial ecosystems. Pteridophytes were even more important in the past, especially before the evolution of the gymnosperms and the flowering plants. This group of land plants were the first plants to evolve roots and leaves, the first to colonize drier habitats, and the first to form forests.

Historically, the research communities interested in extant pteridophytes and those studying the fossil ones were largely separate from each other. The extant and fossil specimens were housed in different facilities (herbaria and paleontological museums, respectively) and their researchers often worked in different departments. The Pteridophyte Collections Consortium (PCC) was created to promote the integration of these communities by bringing together specimen data and associated resources for both living and fossil pteridophytes.

The Pteridophyte Collections Consortium TCN is a three-year project funded through the National Science Foundation Advancing the Digitization of Biological Collections program (ADBC) to digitize and web-mobilize over 1.6 million extant and fossil pteridophytes from 36 herbaria and museums throughout the U.S. In the future, we hope to include collections from new PCC-affiliated institutions as that will join us as Partners to an Existing Network (PEN), and to collaborate with other institutions worldwide. One of our primary goals is to database and image these collections to make them web-accessible to researchers and the public alike. Data access is available through our PCC Symbiota portal, and data aggregator sites such as iDigBio, the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EOL), Paleobiology Database (PBDB), iDigPaleo and others. These data are and will be used for research, education and public outreach, and provide for a long-term digital collection archive.
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PCC Symbiota portal: an open source content management system for curating specimen- and observation-based biodiversity data